How we cite our quotes: All quotations are from The Matrix.
Quote #1
RHINEHART: The time has come to make a choice, Mr. Anderson. Either you choose to be at your desk, on time, from this day forth; or you choose to find yourself another job.
Okay, this is a very jerk-boss rhetorical question kind of thing to say. It's not really a choice at all. He's saying show up on time or you're fired. However, it's written as the first binary decision with which Neo is presented and, to the surprise of his boss, Neo is actually going to take the first option.
Quote #2
MORPHEUS: There are two way's out of this building: one is that scaffold, the other is in their custody. You take a chance either way. I leave it to you.
Okay, here we have the first real choice Neo has to make. He tries to be brave but he fails and surrenders to the agents. It's easy to say he made the wrong choice here (no one likes getting bugged) but then again, if he would have fallen off the building that would have been a pretty short movie.
Quote #3
MORPHEUS: This is your last chance. After this there is no turning back. You take the blue pill, the story ends. You wake up in your bed and believe… whatever you want to believe. You take the red pill, you stay in wonderland; and I show you how deep the rabbit hole goes.
This is the ultimate choice of the movie. The two options are very visually real: the opposing red and blue pill and two different Neos, each reflected in one of Morpheus sunglass lenses. There are two clear paths and Neo has the agency to pick either one. Or he could just not take either. Didn't his mother teach him not to take candy from strangers?